MTL-PlotCounter: Multitask Driven Soybean Seedling Counting at the Plot Scale Based on UAV Imagery

Accurate and timely estimation of soybean emergence at the plot scale using unmanned aerial vehicle (UAV) remote sensing imagery is essential for germplasm evaluation in breeding programs, where breeders prioritize overall plot-scale emergence rates over subimage-based counts. This study proposes PlotCounter, a deep learning regression model based on the TasselNetV2++ architecture, designed for plot-scale soybean seedling counting. It employs a patch-based training strategy combined with full-plot validation to achieve reliable performance with limited breeding plot data. To incorporate additional agronomic information, PlotCounter is extended into a multitask learning framework (MTL-PlotCounter) that integrates sowing metadata such as variety, number of seeds per hole, and sowing density as auxiliary classification tasks. RGB images of 54 breeding plots were captured in 2023 using a DJI Mavic 2 Pro UAV and processed into an orthomosaic for model development and evaluation, showing effective performance. PlotCounter achieves a root mean square error (RMSE) of 6.98 and a relative RMSE (rRMSE) of 6.93%. The variety-integrated MTL-PlotCounter, V-MTL-PlotCounter, performs the best, with relative reductions of 8.74% in RMSE and 3.03% in rRMSE compared to PlotCounter, and outperforms representative YOLO-based models. Additionally, both PlotCounter and V-MTL-PlotCounter are deployed on a web-based platform, enabling users to upload images via an interactive interface, automatically count seedlings, and analyze plot-scale emergence, powered by a multimodal large language model. This study highlights the potential of integrating UAV remote sensing, agronomic metadata, specialized deep learning models, and multimodal large language models for advanced crop monitoring.